2C0B

Catalytic domain of E. coli RNase E in complex with 13-mer RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of E. Coli Rnase E Catalytic Domain and Implications for RNA Processing and Turnover

Callaghan, A.J.Marcaida, M.J.Stead, J.A.Mcdowall, K.J.Scott, W.G.Luisi, B.F.

(2005) Nature 437: 1187

  • DOI: 10.1038/nature04084
  • Primary Citation of Related Structures:  2BX2, 2C4R

  • PubMed Abstract: 
  • The coordinated regulation of gene expression is required for homeostasis, growth and development in all organisms. Such coordination may be partly achieved at the level of messenger RNA stability, in which the targeted destruction of subsets of tran ...

    The coordinated regulation of gene expression is required for homeostasis, growth and development in all organisms. Such coordination may be partly achieved at the level of messenger RNA stability, in which the targeted destruction of subsets of transcripts generates the potential for cross-regulating metabolic pathways. In Escherichia coli, the balance and composition of the transcript population is affected by RNase E, an essential endoribonuclease that not only turns over RNA but also processes certain key RNA precursors. RNase E cleaves RNA internally, but its catalytic power is determined by the 5' terminus of the substrate, even if this lies at a distance from the cutting site. Here we report crystal structures of the catalytic domain of RNase E as trapped allosteric intermediates with RNA substrates. Four subunits of RNase E catalytic domain associate into an interwoven quaternary structure, explaining why the subunit organization is required for catalytic activity. The subdomain encompassing the active site is structurally congruent to a deoxyribonuclease, making an unexpected link in the evolutionary history of RNA and DNA nucleases. The structure explains how the recognition of the 5' terminus of the substrate may trigger catalysis and also sheds light on the question of how RNase E might selectively process, rather than destroy, specific RNA precursors.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE E
L
517Escherichia coli (strain K12)Gene Names: rne (ams, hmp1)
EC: 3.1.26.12
Find proteins for P21513 (Escherichia coli (strain K12))
Go to UniProtKB:  P21513
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP*UP*G)-3'R13synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 196.049α = 90.00
b = 196.049β = 90.00
c = 142.660γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-14
    Type: Initial release
  • Version 1.1: 2015-05-20
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance